Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus)

Abstract

The lineage leading to the white sturgeon (Acipenser transmontanus), the largest freshwater fish in North America, experienced at least two rounds of whole genome duplication, and may exhibit both di- and multi-valent meiotic segregation. This species also exhibits contemporary ploidy variants due to spontaneous autopolyploidy. Nonetheless, as a species with several population segments that exhibit chronic recruitment failure, conservation aquaculture is an important part of their management. To facilitate the development of genetic tools to aid white sturgeon conservation, we present a genome assembly for a white sturgeon from the Snake River, Idaho, USA. Analysis of sequence data used for assembly indicated a haploid genome size of approximately 1.5Gbp, implying octoploidy (8 N) relative to a hypothetical acipenserimorph ancestor, while analysis of heterozygous k-mers from 21 to 41 bp suggest the genome reflects both 4 N and 8 N variants. The final genome assembly, scaffolded using two linkage maps constructed from F1 families, contained 6.26Gbp in 832,145 scaffolds, consistent with published genome size estimates. Conserved ortholog completeness for this genome was high (90.5%; 22.8% single-copy and 67.7% duplicated) and the largest linkage map-based scaffold was 55.2Mbp, though the N50 for this assembly was only 416Kbp, indicating the assembly remains fragmented. We demonstrate the utility of this assembly by identifying genomic regions significantly associated with sex. Genetic markers, designed for inclusion in an amplicon genotyping panel, predicted sex 96.6% and 81.5% correctly in females and males, respectively, providing a strong overall association (P = 0.0054) with some variation by geographic region.